2Z6P

Crystal Structure of the Ufc1, Ufm1 conjugating enzyme 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72931.5M ammonium sulfate, 0.1M MES pH 7.0, 10%(w/v) dioxan, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9637.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.829α = 90
b = 46.829β = 90
c = 143.338γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-60402005-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.900SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.844.599.90.08120.310.515648-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.8699.90.332

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.844.51479978199.90.199760.197640.24316RANDOM25.862
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.11-0.110.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.304
r_dihedral_angle_4_deg16.03
r_dihedral_angle_3_deg13.389
r_dihedral_angle_1_deg5.39
r_scangle_it4.187
r_scbond_it2.665
r_mcangle_it1.505
r_angle_refined_deg1.344
r_mcbond_it1.021
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.304
r_dihedral_angle_4_deg16.03
r_dihedral_angle_3_deg13.389
r_dihedral_angle_1_deg5.39
r_scangle_it4.187
r_scbond_it2.665
r_mcangle_it1.505
r_angle_refined_deg1.344
r_mcbond_it1.021
r_nbtor_refined0.317
r_symmetry_vdw_refined0.233
r_nbd_refined0.204
r_symmetry_hbond_refined0.153
r_xyhbond_nbd_refined0.148
r_chiral_restr0.094
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1341
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing